Hardware tools are important for such work. Software is also crucial. During the first year of the Covid-19 pandemic, a young graduate student named Áine O’Toole, along with other members of Andrew Rambaut’s lab at the University of Edinburgh, developed a tool called PANGOLIN (Phylogenetic Assignment of Named Global Outbreak Lineages). ). It became one of the most widely used systems for placing new genomes on the SARS-CoV-2 family tree, assigning rational but unmemorable labels (such as B.1.1.7) and contextualizing new variants of the virus when they emerged.
It was Dr. Rambaut, Dr. O’Toole and their lab colleagues who helped locate and track the first major variant, now called Alpha, when it appeared in the South East of England in late 2020 and headed for London. A year later, scientists in South Africa and Botswana, sequencing travelers’ samples discovered another soaring variant called Omicron.
Such rapid variant detection is extremely valuable, but only if the data is quickly converted into clear, actionable guidance. “We still have the important gaps to get it into the clinic,” said Dr. peacock. These gaps include making it easy for public health and medical personnel who are not trained to use the data and the willingness of health care providers such as hospitals to fund such work. “Right now, most of the sequencing outside of Covid-19 is funded by public health agencies and research funding,” she said.
That hasn’t changed since 2014, when Pardis Sabeti, a computational geneticist at Harvard University, led a team of genomic scientists responding to the horrific Ebola virus outbreak in West Africa. They sequenced 99 genomes of the virus, sampled from patients at a hospital in Sierra Leone. Comparing sequences revealed that all of those cases were most likely the result of human-to-human transmission, rather than spillovers from a host in the wild.
The outbreak in West Africa ended after more than 28,000 Ebola cases and 11,000 deaths, at which point genomic epidemiology had proved its worth by revealing how the virus spread. With Covid-19, there are so far 589 million known cases and more than six million deaths. The new discipline can barely keep up with the virus, let alone get ahead of it. Sarah Cobey, an evolutionary biologist at the University of Chicago who works at the intersection of immunology, viral evolution and epidemiology, sees “gaping holes” in the genetic surveillance of Covid-19.
“Although we have a lot of sequences, they are disproportionately from a few locations,” Dr. Coby me. During the first year of the pandemic, Great Britain, New Zealand, Australia and Iceland were among the countries that: sequentially in most cases. The Netherlands and the Democratic Republic of the Congo were also notable for rapid sequencing. As the pandemic progressed, scientists in South Africa undertook a major sequencing effort (as reflected in the initial detection of the beta variant and then of the Omicron), and coverage also improved in Canada and Scandinavia. Other parts of the world remain “blind spots,” said Dr. cobey.
